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Microbial Ecology

Scientists use the latest techniques to understand the living community of microbes in the environment.

Microbiology

Plant-Microbe Interactions

Browse samples of USGS research about microbial ecology and plant-microbe interactions.

Plant-Microbe Interactions in San Francisco Bay Wetland Sediments: Impacts on Mercury Biogeochemistry
Lisamarie Windham-Myers in a pickleweed (Salicornia spp.) dominated marsh near Petaluma River, California, with one of the ‘devegetation’ plots used to examine plant-microbe interactions. Photo credit: USGS
Lisamarie Windham-Myers in a pickleweed (Salicornia spp.) dominated marsh near Petaluma River, California, with one of the ‘devegetation’ plots used to examine plant-microbe interactions. Photo credit: USGS
Dense root biomass associated with white rice. Photo credit: Mark C. Marvin-DiPasquale, USGS
Dense root biomass associated with white rice (Oryza sativa) from agricultural fields of the Yolo Bypass in California’s central valley, a study site used to explore the linkage between emergent plants, microbial activity and methylmercury production. Photo credit: USGS
Image Gallery

Wetland vegetation density and type can influence key microbial processes both through the resupply of key electron acceptors (e.g. sulfate) and the release of electron donors (e.g. acetate and low molecular weight organics) that fuel microbial processes. Conversely, microorganisms are involved in the generation of compounds that are both stimulatory (e.g. the generation of ammonium) and inhibitory (e.g. the generation of sulfide) to plant growth. Due partially to enhanced microbial activity associated with the root zone (rhizosphere) of emergent wetland plants, wetland environments are generally known to be zones of enhanced methylmercury (MeHg) production. However, the extensive variation in wetland types, as dictated by variations in hydrology, salinity and dominant plant species, leads to a wide range in microbial MeHg production rates. The San Francisco Bay watershed is contaminated with mercury as a result of historic mining practices, making the need to better understand the linkages between wetland plants and the microbial community that produces MeHg from inorganic mercury, particularly relevant. Experimental and comparative studies throughout the SFB region have demonstrated that active photosynthetic organic inputs through live roots and into the rhizosphere promote biogeochemical and microbial processes that in turn lead to enhanced MeHg production. Further, plant root density has been found to be proportional to the activity of the microbes associated with MeHg production, across a range of SFB wetland types. Thus, the structural and physiological characteristics of plants also may be also useful in developing landscape-scale predictions of MeHg production in wetland settings. Ongoing studies in a range of SFB wetland types – from freshwater natural floodplains and flooded agricultural fields to saltmarshes – seek to develop a more quantitative understanding of the these plant-microbe relationships, and their impact on MeHg production and export, in this historically mercury contaminated ecosystem.

Publications:

Windham-Myers, L., M. Marvin-DiPasquale, D.P. Krabbenhoft, J.L. Agee, M.H. Cox, P. Heredia-Middleton, C. Coates, and E. Kakouros. 2009. Experimental removal of wetland emergent vegetation leads to decreased methylmercury production in surface sediments. Journal of Geophysical Research 114, G00C05, doi:10.1029/2008JG000815

For more information contact Lisamarie Windham-Myers and Mark C. Marvin-DiPasquale, Menlo Park Regional Office.

See also Geomicrobiology: Mercury >>

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Symbiosis on Mt. Everest
In 2011, a USGS scientist (Rusty Rodriguez) teamed up with ASC adventures to isolate plants growing at the highest elevations on earth.
a. In 2011, a USGS scientist (Rusty Rodriguez) teamed up with ASC adventures to isolate plants growing at the highest elevations on earth. (see powerpoint for more details)
The plants were identified as a moss species and found to be symbiotic with microscopic fungi living entirely inside plant tissues. This is the first documentation of this high elevation symbiosis.
c. The plants were identified as a moss species and found to be symbiotic with microscopic fungi living entirely inside plant tissues. This is the first documentation of this high elevation symbiosis.
The plants were collected and photo-documented using scientific protocols provided by Rodriguez and shipped to the Western Fisheries Research Center for analysis.
b. The plants were collected and photo-documented using scientific protocols provided by Rodriguez and shipped to the Western Fisheries Research Center for analysis.

USGS scientists from Dr. Russell Rodriguez Laboratory are conducting research on plants from Mt Everest. The plants collected at 21,000 ft are likely the highest growing plants on earth. The habitat imposes extreme temperatures, high uv, desiccation and wind. Researchers are determining if the ability of the plants to tolerate these stresses is due to fungal endophytes.

In every ecosystem the team has studied to date researchers have found that plants do not adapt themselves to abiotic stresses. Instead, they form symbiotic associations with fungal endophytes that confer stress tolerance. Based on this observation, the team has developed a new strategy (Symbiogenics) to mitigate impacts of climate change on plants, enhance habitat restoration success, and manage invasive species. The Mt Everest project is a collaboration with a new nonprofit organization (Adventurers and Scientists for Conservation). For more information, see powerpoint, or contact Rusty Rodriquez.

 

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Urban Salt Marsh Restoration: Crissy Field, Golden Gate National Recreation Area
At the foot of San Francisco’s historic Presidio, Crissy Marsh consists of a mix of subtidal, intertidal and upland habitats. Photo Credit: Lisamarie Windham-Myers, USGS
At the foot of San Francisco’s historic Presidio, Crissy Marsh consists of a mix of subtidal, intertidal and upland habitats. Photo Credit: Lisamarie Windham-Myers, USGS
Water sampling the Crissy Marsh inlet to the San Francisco Bay, with Alcatraz Island seen in the background. The inlet is subject to periodic closure events, resulting from longshore sand migration and a muted tidal prism. Photo Credit: Hillary Harms, USGS
Water sampling the Crissy Marsh inlet to the San Francisco Bay, with Alcatraz Island seen in the background. The inlet is subject to periodic closure events, resulting from longshore sand migration and a muted tidal prism. Photo Credit: Hillary Harms, USGS

As part of the Golden Gate National Recreation Area, Crissy Field is a popular recreational destination in San Francisco, California, for both residents and tourists. The restoration of 18-acres of historic tidal marsh at this site has had great success in terms of public outreach and visibility, but less success in terms of revegetated marsh sustainability. Native cordgrass (Spartina foliosa) has experienced dieback and has failed to recolonize following extended flooding events resulting from periodic closures of the inlet channel, which inhibits daily tidal flushing. These inlet closure events are attributed to the marsh’s small tidal prism and to sand deposition near the inlet mouth. The National Park Service (NPS) currently manages the marsh by dredging the inlet channel to reinstate tidal flow approximately once per year during the spring (at the beginning of the active growing season). The joint USGS-NPS Water Quality Monitoring Program is sponsoring ecosystem-level research at the Crissy Field marsh to help advise NPS wetland managers as to the impacts of these closure events on marsh sustainability, both in terms of plant stress (e.g. fermentative respiration) and the microbial cycling of sulfur and mercury. Specifically we are investigating to what extent closure events are associated with a) increased reduced sulfur concentrations (generated by microbial sulfate reduction) in sediment and pore water, which might be toxic to juvenile or newly recolonized plants, and b) increased toxic methylmercury production by microbes in the sub-tidal and intertidal zones. This research, and that of collaborators in USGS Coastal and Marine Geology, is providing a scientific basis for determining how rapidly and how often to dredge the tidal channel after a closure event, and to inform habitat enhancement projects including a current design to daylight a perennial creek that drains into the marsh and to expand transitional wetland habitats.

Related Links:

For more information contact Lisamarie Windham-Myers, Menlo Park Regional Office, Mark C. Marvin-DiPasquale, Menlo Park Regional Office, and Kristen Ward, NPS Golden Gate National Recreation Area (NPS-GGNRA).

See also Ecosystem Function: Habitat Restoration >>
See also Geomicrobiology: Mercury >>

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